--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FCSConvert.R	Mon Jun 22 17:26:06 2020 -0400
@@ -0,0 +1,151 @@
+#!/usr/bin/env Rscript
+# ImmPort FCSConvert
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+#
+# Converts the FCS file to text without transformaton
+# To run in R
+# 1) library(flowCore)
+# 2) source("FCSConvert.R")
+# 3) transformFCS("filename")
+#
+# Version 1.4.1
+# March 2016 -- added lines to run directly from command line
+#
+
+library(flowCore)
+
+convertFCS <- function(fcs,compensate=FALSE,debug=FALSE) {
+  # Check file type and FCS version
+  if (class(fcs)[1] != "flowFrame") {
+    print("convertFCS requires flowFrame object as input")
+    return(FALSE)
+  }
+
+  keywords <- keyword(fcs)
+  markers <- colnames(fcs)
+  print_markers <- as.vector(pData(parameters(fcs))$desc)
+  # Update print_markers if the $P?S not in the FCS file
+  for (i in 1:length(print_markers)) {
+    if (is.na(print_markers[i])) {
+      print_markers[i] <- markers[i]
+    }
+  }
+
+  if (debug) {
+    print("****Inside convertFCS")
+    print(paste("    FCS version:", keywords$FCSversion))
+    print(paste("    DATATYPE:", keywords['$DATATYPE']))
+  }
+
+  if (keywords$FCSversion == "2" ||
+      keywords$FCSversion == "3" ||
+      keywords$FCSversion == "3.1" ) {
+      datatype = unlist(keywords['$DATATYPE'])
+    if (datatype == 'F') {
+        # Apply compensation if available and requested
+      spill <- keyword(fcs)$SPILL
+      if (is.null(spill) == FALSE && compensate == TRUE) {
+        if (debug) {
+          print("Attempting compensation")
+        }
+        tryCatch({ fcs = compensate(fcs, spill) },
+                   error = function(ex) { str(ex); })
+      }
+      # Process fcs expression data, using transformation
+      # based on category of the marker.
+      fcs_exprs <- exprs(fcs)
+      colnames(fcs_exprs) <- print_markers
+        } else if (datatype == 'I') {
+          fcs_exprs <- exprs(fcs)
+          colnames(fcs_exprs) = print_markers
+        } else {
+          print(paste("Data type", datatype, "in FCS 3 is not supported"))
+          fcs_exprs <- FALSE
+        }
+  } else {
+    print(paste("FCS version", keyword(fcs)$FCSversion, "is not supported"))
+    fcs_exprs <- FALSE
+  }
+  fcs_exprs
+}
+
+
+#
+# Starting function for processing a FCS file
+#
+processFCSFile <- function(input_file, output_file="",
+                           keyword_file="",compensate=FALSE, debug=FALSE) {
+
+  #
+  # Generate the file names for the output_file and keyword_file
+  #
+  pieces <- unlist(strsplit(input_file, .Platform$file.sep))
+  filename <- pieces[length(pieces)]
+
+  if (output_file == "") {
+    filepieces = unlist(strsplit(filename, '\\.'))
+    #replace .fcs with .txt; append .txt if not ending in .fcs
+    if (filepieces[length(filepieces)] == 'fcs') {
+      filepieces[length(filepieces)] <- 'txt'
+    } else {
+      filepieces[length(filepieces)+1] <- 'txt'
+    }
+    output_file <- paste(filepieces, collapse = '.')
+  }
+
+  if (keyword_file == "") {
+    filepieces <- unlist(strsplit(filename, '\\.'))
+    #replace .fcs with .keyword; append .keyword if not ending in .fcs
+    if (filepieces[length(filepieces)] == 'fcs') {
+      filepieces[length(filepieces)] <- 'keyword'
+    } else {
+      filepieces[length(filepieces)+1] <- 'keyword'
+    }
+    keyword_file <- paste(filepieces, collapse = '.')
+  }
+
+  if (debug) {
+    print (paste("Converting file: ",input_file))
+    print (paste("Original file name: ",filename))
+    print (paste("Output file name: ",output_file))
+    print (paste("Keyword file name: ",keyword_file))
+  }
+  fcs <- read.FCS(input_file, transformation=F)
+  keywords <- keyword(fcs)
+  write.table(as.matrix(keywords),file=keyword_file, quote=F,
+              row.names=T, col.names=F, sep='=', append=F)
+
+  transformed_data <- convertFCS(fcs,compensate,debug)
+  write.table(transformed_data, file=output_file, quote=F,
+              row.names=F,col.names=T, sep='\t', append=F)
+}
+
+# Convert FCS file without transformation
+# @param input_file     FCS file to be transformed
+# @param output_file    FCS file transformed ".txt" extension
+# @param keyword_file   FCS file keywords ".keywords" extension"
+# @param compensate     Flag indicating whether to apply compensation
+#                       matrix if it exists.
+transformFCS <- function(input_file, output_file="",
+                         compensate=FALSE, keyword_file="", debug=FALSE) {
+
+  isValid <- F
+  # Check file beginning matches FCS standard
+  tryCatch({
+    isValid <- isFCSfile(input_file)
+  }, error = function(ex) {
+    print (paste("    ! Error in isFCSfile", ex))
+  })
+
+  if (isValid) {
+    processFCSFile(input_file, output_file, keyword_file, compensate, debug)
+  } else {
+    print (paste(input_file, "does not meet FCS standard"))
+  }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+transformFCS(args[1], args[2], args[3])